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- PDB-2l9f: NMR solution structure of meACP -

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Basic information

Entry
Database: PDB / ID: 2l9f
TitleNMR solution structure of meACP
ComponentsCalE8
KeywordsTRANSFERASE / Acyl Carrier Protein / Micromonospora echinospora
Function / homology
Function and homology information


transferase activity
Similarity search - Function
: / ACP-like / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension ...: / ACP-like / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / HotDog domain superfamily / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Beta-ketoacyl synthase / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMicromonospora echinospora (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsLim, J. / Yang, D. / Liang, Z.X. / Kong, R. / Murugan, E. / Ho, C.L.
CitationJournal: Plos One / Year: 2011
Title: Solution structures of the acyl carrier protein domain from the highly reducing type I iterative polyketide synthase CalE8
Authors: Lim, J. / Kong, R. / Murugan, E. / Ho, C.L. / Liang, Z.X. / Yang, D.
History
DepositionFeb 8, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 27, 2012Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CalE8


Theoretical massNumber of molelcules
Total (without water)11,2231
Polymers11,2231
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein CalE8 / meACP


Mass: 11222.643 Da / Num. of mol.: 1 / Fragment: UNP residues 925-1017
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: Q8KNG1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HN(CO)CA
1413D HNCA
1513D MQ (H)CCH-TOCSY
1614D 13C,15N edited-NOESY

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Sample preparation

DetailsContents: 50mM sodium phosphate; 50mM sodium chloride; 1mM DTT; 1mM EDTA; 1mM [U-99% 13C; U-99% 15N] meACP; 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium phosphate-11
50 mMsodium chloride-21
1 mMDTT-31
1 mMEDTA-41
1 mMmeACP-5[U-99% 13C; U-99% 15N]1
Sample conditionspH: 6.85 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRspyZheng Yuchemical shift assignment
NMRspyZheng Yupeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxgeometry optimization
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thodata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
MOLMOLKoradi, Billeter and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsProtein phi angle constraints total count: 62 / Protein psi angle constraints total count: 63
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 3.74 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Maximum torsion angle constraint violation: 4.18 ° / Representative conformer: 1 / Torsion angle constraint violation method: CYANA

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